Year One / First Quarter Progress Report May 31, 2011

stalliongrapevineΒιοτεχνολογία

1 Οκτ 2013 (πριν από 4 χρόνια και 11 μέρες)

112 εμφανίσεις


Year One /

First Quarter

Progress

Report

May 31, 2011

“TRPGR

IOS
-
1025974
:
Comparative genomics of environmental stress responses
in North American hardwoods



Introduction

This project is focused on genomic resource building for a range of North American hardwood
species.
This
first progress
report summarizes the
activities and results of project personnel for
the first quarter of this grant period (2/1/2011


5/1/2011) as well as progress achieved pre
-
award. Consequently, the report will reflect
progress toward
the project objectives by presenting
materials on th
e subjects of 1) population development, 2) EST library construction, 3) BAC
library construction, and 4) genetic/QTL map construction
, 5) bioinformatics/website
development, 6) outreach and 7)

project management
.



Abbreviations: PSU


Pennsylvania Stat
e University; UT


University of Tennessee; MU


Missouri University; UWA


University of West Alabama; ND


University of Notre Dame;
MTU


Michigan
Technological University; CLM


Clemson University



Activities


Population Development



Mapping populat
ions


Black Walnut (MU
/ND
)


Mapping Population:
Seed was collected f
or this species in the fall
2008, from two trees growing in a clonal repository containing 22 nut cultivars at the University
of Missouri (MU) Horticulture and Agroforestry

Research Center (HARC) in New Franklin,
MO. This specific repository is the oldest of four such plantings containing a total of 100
accessions, selected for an array of commercial nut traits, as part of an ongoing breeding
program which has been sponsore
d by the University of Missouri Center for Agroforestry since
2000.


Since June 2009, in collaboration with Dr. Romero
-
Severson at the University of Notre Dame
(ND), we have been successful in identifying a total of 320 full sib
seedlings

representing the
cross between ‘Sparrow’ x ‘Schessler’ based on a panel of five DNA markers

(using CERVUS
3.0)
. These 320 full sibs represent 31.7% of the total of 1010 seedlings genotyped so far. To
date, 288 of these full sib individuals have been planted at HARC.


P
rior to establishment at HARC with the rest of the mapping population,

60 ‘Sparrow’ x
Schessler’ full sibs
were used
by Dr. Haiying Liang’s lab at Clemson
(
summer 2010
)
for stress
treatments and RNA extraction
to contribute to
transcriptome sequencing.


Northern Red Oak
(UT
)
-

Mapping Population

:

Open
-
pollinated seed
s

from a select red oak
tree growing at Purdue University campus have been collected on several occasions over the last
10 years and subjected to parental analysis using a marker screen to i
dentify full
-
sib progeny for
genetic mapping. Seedlings from multiple cohorts have been raised at the University of
Tennessee. This spring, s
creens protecting the smaller

trees in these plantations were

removed to
stimulate growth.
Plantations have been
monitored and maintained.


Seedlings from this same cross
are being
used for stress testing, RNA extraction, and EST library
construction at Clemson (this quarter).
P
rogeny exclusion

using the
5 marker multiplex progeny
exclusion kit
developed
for
northern

red oak

has been used to identify full
-
sibs from
535 half
-
sib
acorns
collected from the
SM1

parent’s
2010 progeny
.
Almost 90% of the samples on
the
first
plate
tested
(92 samples) were full sibs. This is exceptionally high, but rescoring all
chro
matograms manually produced the same result.



Sweetgum (MU)



Mapping Population:

Open pollinated seeds were collected from a single
ramet growing in an isolated clonal seed orchard in southern Indiana. This orchard contains a
total of 16 clones that we
re originally selected for their winter hardiness within a
provenance/progeny test established by Michigan State University. These selections were made
by Dr. Coggeshall in 1996. As of this writing, these seeds are still in stratification, and will be
so
wn in the greenhouse in late May 2011. Seedlings will be subjected to genotyping and
paternity analysis to identify a full
-
sib cohort for mapping.


Honeylocust (UT
/MTU
)



Mapping Population
:
Seed was collected from a single tree in central
Tennessee in
autumn
2008
,

treated with muriatic acid to increase water permeability of the seed
coat and pla
nted in raised nursery beds at UT. Seed
germinated
over two years

(
2009 and 2010
)
.
Seedlings from the 2009 crop were potted during the dormant season
, and l
eaf
samples were
taken at the end of the 2010 summer for DNA extraction and
genotyping to determine paternal
contributions (MTU)
. A mapping population
consisting
of 402
full
-
sibs were identified and

established at the East Tennessee State Nursery in Fe
bruary,

2011
.
T
he plantation was attacked
by voles soon after planting
, with a modest loss

(mortality
-

four trees
, damaged


unknown)
.



Yellow
-
Poplar (UT)



Mapping population
:
Open
-
pollinated seed was collected from
a single
c
lone
(#
108
) in a yellow poplar s
eed orchard

in the 2010 autumn, stratified, and sent to Dr. Liang
(Clemson)
in January,

2011 for germination on

vermiculite. L
ow germination rate
s

of about 7%

were observed
.
Approximately 20 seedlings have been obtained to date. This material may not
serve

our needs. But alternatives exist.



Controlled crosses between Clone 108 and Clone 23 (
male) were made in late April (2011). The
parent trees were damaged during a major tornado/hailstorm outbreak and cross success is
currently unknown.
Clone 108 ha
s been
re
-
grafted
to preserve the genotype, as ramets in the

Knoxville

yellow
-
poplar orchard are

very old (established in 1
966) and declining in health
.



Yellow
-
Poplar
MU



As a backup to the breeding efforts undertaken at UT, open pollinated
seeds were collected from a single tree growing at HARC in the fall 2010 and sown at the
Vallonia State Nursery in southern Indiana on November 1
st
. The resulting seedling will be
li
fted in the spring 2012. It is anticipated that the ability to identify full sibs within this open
pollinated family will be facilitated by the fact that yellow
-
poplar is represented by a total of
only four mature trees at this site.



Population Develop
ment




The following populations are being created
as a resource for
the construction of genetic linkage
maps in future research. These seedlings will be used for the collection of
DNA/RNA for BAC
library construction and transcriptome sequencing.

The R
NA sequence will provide genetic
markers for the construction of genetic maps and association studies, The BAC libraries will
enable the construction of physical maps in the future. Screening for full
-
sibs from these
populations will progress as funds an
d time permit.


Green Ash (MU)



Open pollinated seeds were collected from a single tree growing on the MU
campus in the fall 2010 and sown at the Vallonia State Nursery in southern Indiana on November
1
st
. The resulting seedling will be lifted in the s
pring 2012.


Sugar Maple (MU)

-

Open pollinated seeds were collected from a single tree growing on the
MU campus in the fall 2010 and sown at the Vallonia State Nursery in southern Indiana on
November 1
st
. The resulting seedling will be lifted in the spri
ng 2012.


(Non
-
project supported activity)

Black Gum (MU)

-

Open pollinated seeds were collected in the fall 2009 from a single tree
located in a city park in Columbia, MO (which is outside the native range for this species). A
total of five mature black
gum trees are growing in this park, which should facilitate the
identification of full sib individuals within this open pollinated family. To date, a total of 140
containerized seedlings have been produced, which are currently growing at HARC. Plans call

for an additional seed collection and sowing in the fall 2011.


EST Library / Transciptome Sequencing

(Clemson
/ND
)

Black walnut tissue collection

(ND)
.

T
issue
was
collected
from

leaves, buds, twigs, cambium, sapwood, nutlets, paper
-
punch
wounded leaves
and wounded twigs

from one tree of the cultivar Sparrow, the female parent of
the mapping population
.

All tissue
s

w
ere

flash frozen in separate tubes and delivered to Haiying
Liang at Clemson.

This material will be used for RNA extraction and cDNA produc
ed for
transcriptome sequencing.

Northern red oak tissue collection.

T
issue
has been collected
from SM1, the female parent of the
northern red oak
mapping
population.
Samples were
collected
from
leaves, buds, twigs, cambium, sapwood,

paper
-
punch
wounded leaves and wounded twigs. All tissue
s

w
ere

flash frozen in separate tubes and
are
stored i
n our
-
80 freezer at Notre Dame for sequencing.


In addition to the baseline materials just described, cDNA libraries are being
developed
from
full
-
sib progeny of the parent trees. These progeny are being subjected to stress treatments to
provide contrasting transcriptome
profiles
.


S
tress treatments
.

S
tress treatments

were completed on full
-
sib progeny for both

black walnut and northern r
ed oak.
Treatments included
wounding, cold, heat, and drought
.

RNA extraction from the stressed
-
treated northern red oak seedlings is in progress. This RNA will contribute to the mRNA
extracted from multiple tissue types in the NRO mother tree SM1


For ea
ch species, 10 full
-
sib seedlings
were used for wounding, cold, heat, and drought
treatments. Another 10 seedlings were included as control.

For black walnut, t
wo

year
-
old full
-
sib seedlings

from MU were used, and returned for planting in the mapping trial
s
.
For northern
red
oak,
stratified full
-
sib northern red oak acorns
,

provided by
ND, were grown

in

the
greenhouse

at Clemson for two months (see photo) prior to

treatment.
For each treatment and the control,

l
eaves and fine white roots were
collected
fro
m all t
en seedlings
, except for the wounding treatment,
in which only leaves were collected. A total of 90 samples were
collected for
each species
. All samples are stored in
-
80 °C until
RNA extraction.


RNA extraction protocols and recovery

Total RNA were extracted from individual samples
using

the RNAqueous®
-
Midi kit (Ambion,
catalog #1911), while mRNA were isolated with the Poly(A) Purist™ mRNA Purification Kit
(Ambion, catalog #1916). Both total RNA and mRNA were checked on an Agilent 2100

Bioanalyzer (Agilent Technologies) for quality and concentration. DNase treatments were
conducted before and after mRNA isolation. The amounts of mRNA obtained for each tissue
type
in black walnut
are listed in Table 1.

RNA extraction
s

from the treated a
nd control northern
red oak tissues are underway
.

Table 1. The amounts (
µ
g) of mRN
A

obtained from each black walnut samples.


Control

Wounding

Heat

Cold

Drought


Leaf

Root

Leaf

Leaf

Root

Leaf

Root

Leaf

Root

mRNA

10,320

2,370

2,520

2,265

3,300

1,300

1,260

1,310

lost



BAC Library Construction


No activity

this quarter.


Genetic / QTL Maps

(
M
T
U

/ ND
)


Honeylocust (
Gleditsia triacanthos
)



MTU

: marker development

Leaf samples were collected from the seed parent, six putative pollen parent
s

and 432 progeny
by Scott Schlarbaum
between August 30 and
September

1, 2010
and shipped to Michigan
Technological University. All samples were prepared for DNA isolation in a 96
-
well plate
format (DNeasy 96 plant kit, Qiagen)

and are stored at
-
80 °C
. DNA

was isolated from the seed
parent, the putative pollen parent and 16 progeny for primer testing.


A total of
14

published EST
-
SSRs markers have been tested for amplification in the seed parent
and putative pollen parents including
8

markers originally dev
eloped for
Medicago trunculata

(Eujayl et al. 2004, Gupta and Prassad 2009) and
6

markers originally developed for
Ceratonia
siliqua

(Caruso et al. 2008), a member of the same subfamily (Caesalpinioideae) as
Gleditsia
triancanthos
(Wojciechowski et

al. 2004). In addition, 126 new EST
-
SSR primer pairs have been
derived from
the

published EST library in
Ceratonia siliqua

(Caruso et al. 2008) by Meg Staton.
Until now,
48 markers have been ordered and 24

of these markers have been tested for
amplificatio
n and polymorphism
in honeylocust
after gel electrophoretic

separation

on the
Qiaxcel capillary analyzer
(Qiagen)
using the high resolution
kit
.

None of the published EST
-
SSR markers showed amplification in honeylocust. Out of the
24

new EST
-
SSRs test
ed
,
7

showed amplification in honey
locust and
4

were polymorphic.


Northern red oak

(
Quercus rubra
)

MTU: marker development

A total of 48 EST
-
SSRs markers (4 markers
on each linkage

group) originally developed for
Q.
robur

were ordered (Durand et

al. 2010).
28

markers have been amplified
and tested for
polymorphism
in the crossing parent
s

of the
Q. rubra

full
-
sib family (provided by Jeanne
Romero
-
Severson).
Seventeen

of the
28

markers tested amplified a product of the expected size,
and
10

markers were polymorphic

in the
Q. rubra

crossing parents
.
5

markers were heterozygous
for only one parent tree

(4 for the male parent, 1 for the female parent) and

5

markers were
heterozygous for different alleles in both parents.
These markers will enab
le comparative studies.


Bioinformatics / Website Development

(CLM)

Creation of project website

The domain name
www.hardwoodgenomics.org

was purchased for 5 years. A password
protected development website wa
s created and shared with the project PIs
(
dev.hardwoodgenomics.org
, username: NSFhardwood, password: tr33s
!
). This site is based on
Drupal, a p
opular open
-
source content management system. The software Tripal, initially
developed for Fagaceae Genomics Web, has been installed as well. After initial approval of
design and content from the project PIs, the site will become public.



Results
(completed activities)

Bioinformatics / Website (CLM)

Liriodendron cDNA sequence assembly and marker identification

Over 2 million reads were obtained for
Liriodendron tulipifera

from Genbank and the Ancestral
Angiosperm Genome Project. These were trimmed

with the software NGS Backbone and
assembled with the 454 software Newbler into 33,745 isotigs (putative individual transcripts). A
custom SSR script was run to identify short tandem repeats and examine underlying sequence
assemblies to detect evidence
for polymorphism. Of 9,471 SSRs identified with primers, 3,177
show evidence of polymorphism in the sequence data.


The 2 million reads were realigned to the isotigs to detect SNPs with 454 software
. After
filtering for at least 10 nucleotides at the SNP position and at least 25% of reads containing the
minor variant, 27,159 SNPs were identified.


Identifying SSRs from a species
related
to Honeylocust

No ESTs are currently available for
Gleditsia
triacanthos
. However
Ceratonia siliqua
,
commonly known as carob, is in the same clade as honeylocust and has 1393 public ESTs in
Genbank
. The sequences were assembled with cap3 at 95% identity to remove any redundancy
in the data set. 126 SSRs were ident
ified in the nonredundant data set of 1,131 sequences.
Primers were designed with the software Primer3. These
are
be
ing

used to test for markers in
honeylocust.



[Interim results]

Interim results for other activities have been included in the “Activit
ies” section of this report
due to their incomplete status.

Anticipated Activities (Next Quarter)


Population Development


Black Walnut

(MU)


Additional full sibs will be established in the two mapping population
outplanting

sites in a timely fashion as fingerprinting results are obtained from Dr. Romero
-
Severson lab at ND.


Green Ash

(MU)



All potential pollen parents, plus the maternal tree used as the source of the
mapping population individuals will be sampled (leaf samp
les) in the summer 2011 and sent to
Dr. Romero
-
Severson’s lab at ND for genotyping and parental ana
l
ysis.


Honeylocust

(UT)
-

W
e
will
sample leaves
for
Dr. Gailing
from an additional 20
-
25 trees in
order to have a population sample

from the general area of

the mother tree
. Also,
for
construct
ion of the BAC
DNA library
, tissue will be taken

from the mother tree

before dawn.
Arrangements will be made to take samples in
early
May for both of these purposes. Population
samples will be sent directly to Dr. Ga
iling. For the
c
DNA library sample, we will visit the tree
prior to dawn and cut branches with leaves. The branches will be placed in
a
container

with ice
and sealed with duct tape. It will be transported to Knoxville

and given Dr. Liang’s personnel

for

further transport to Clemson.


DNA samples of leaf tissue will be taken
from all
unsampled honeylocust seedlings growing in
Knoxville. The samples will be sent to Dr. Gailing for analysis.


The seed crop of the mother tree will be assessed during the sum
mer
,

and additional seed will be
collected in the autumn when mature, if there is a crop.


Voles
attacking the mapping population
will be controlled with wheat seed that has been
impregnated with zinc phosphide.


Northern
Red
a
nd White Oak
molecular
mapping populations

(UT)


The plantations will be
maintained by mowing and herbicides during the growing season. The 2007 northern red oak
seedlings will be ro
gu
ed per results from Dr. Romero
-
Severson’s laboratory. The white oak
plantation will be ro
gu
ed

per results from Dr. Carlson’s laboratory.


N
orthern red oak full
-
sibling seedlings from Dr. Liang that have been stress tested

at Clemson
will be transferred to UT
. The seedlings will be grown
in the nursery
for the 201
1 summer,
lifte
d
during the dormant season, and
added to the existing mapping population at Ames Plantation.


Full
-
sibling northern red oak seedlings used for stress tests by Drs. Shumaker and Carlson will
be transferred f
rom Penn State to UT in mid
-
July

and housed for
the remainder of the 2011
growing season.


The seed crop on the white oak mother trees will be assessed during the

summer in case more
seedlings are needed for the mapping population or other experiments.


Sugar Maple

(MU)



All potential pollen parents
, plus the maternal tree used as the source of the
mapping population individuals will be sampled (leaf samples) in the summer 2011 and sent to
Dr. Romero
-
Severson’s lab at ND for genotyping.


Sweetgum

(MU)



The sweetgum seedlot will be sown in late May a
nd the resulting seedlings
maintained in containers. It is anticipated that leaf samples will be submitted to
PSU
in the
summer
of
2011 to begin the work of identifying full sibs. Leaf samples from all clones in the
Indiana seed orchard will also be coll
ected in the summer 2011 for use in the identification of
full sibs.


Yellow
-
poplar

(UT)


Breeding will continue until flowering has ceased. The resulting seed
crop will be assessed in mid
-
May.


Leaf samples for DNA extraction wi
ll be taken from Clone 23

and

transport
ed

to Clemson at the
same time of the honeylocust leaf exchange.


Black Gum

(MU)

-

All potential pollen parents, plus the maternal tree used as the source of the
mapping population individuals will be sampled (leaf samples) in the summer 2011 and sent to
Dr. Romero
-
Severson’s lab at ND.


BAC Library Construction


BAC library
construct
ion
will

commence
for Northern red oak

and black walnut during the
coming quarter
.
(CLM
/ND/MU
)


EST Libraries


RNA extraction and cDNA synthesis for Northern red oak

will be completed
(CLM)
.


Research activities at Penn State will commence with the receipt of Black walnut and Northern
red oak RNAs from Clemson University and construction of 454 libraries for DNA sequencing.



Genetic / QTL Maps

(ND, MTU)


Black walnut genetic mapping

We will screen all of our black walnut and butternut microsatellite markers (40 markers) for
informativeness and genotype the informative markers across the mapping population. We will
also extract promising markers from the public databases, focusing fir
st on the
Julgans regia

sequences in GenBank.


Northern red oak genetic mapping

We will genotype the
existing
mapping population with all of our informative northern red oak
microsatellites (50), then proceed to the EST sequences from Q. robur/Q. petraea w
hich Oliver
Gailing sent to us. After that, we will proceed to the EST
-
SSR
markers
available from the
F
agaceae
G
enomics
P
roject
, focusing first on the oak EST
-
SSR. After that, we will include the
SNP data from UCLA.

Marker development continues at MTU.



Honeylocust
(Gleditsia triacanthos)

48

additional
markers

will be tested

for polymorphism
in the seed parent and in the putative
pollen parents
. Polymorphic markers will be characterized in a larger population sample (24
indiv
id
uals). DNA will be isolated from all samples (parent trees and progeny).
We will develop
a set of markers that

will be used to identify full
-
sib families by paternity exclusion among the
progeny of 432 seedlings that were collected from the same mother tre
e.



Bioinformatics / Website (CLM)




PI Staton

will attend the ForestTrac
workshop
on

Interoperability and Integration of
Databases in Europe and North America” from May 23
-
24
th

in Baden, Austria.



Launch of the Project (Abbreviated here as the Hardwood
Genomics Project (HGP)) website
to the public.



Expansion of the HGP website to include the Liriodendron transcriptome sequences,
assembly, functional annotation and mined markers.



Inclusion of the data from the Fagaceae Genomics Web into HGP website.



Devel
oping use case scenarios for the new mapping, marker and phenotype section of the
website. This will include answering the following questions:

o

What types of data do the mapping PIs currently store? What format is it in?

o

How can this data be appropriatel
y stored in the chado database schema?

o

What types of data would breeders (traditional and marker
-
assisted) like to access?
What display and download formats would be the most useful?

o

What types of searches would users perform to access this data?








Outreach


UT / ND


Genomic / Genetic / Forestry Training for Cherokee Tribal Youth

As part of a comprehensive outreach plan to develop field and classroom activities that can be
delivered to eastern band of the Cherokee tribes in North Carolina, PI’s Schlarbaum and

Romero
-
Severson
have hosted multiple

conference call
s and
attended
one s
ite visit

with
Carmaleta Monteith, curriculum designer for the new Ravensford School (K
-
12 grades) in
Cherokee
, NC
.
PI Schlarbaum

presented a
n invited

seminar on exotic forest pests
and related
research to an audience that included tribal members, Cherok
ee artisans, BIA forestry personnel,
the Tribal (Eastern Band of Cherokee Indians) Forester (Mr. Tommy Cabe), and the Ravenford
School’s forestry class and their instructor. He was invited by
the Revitalization of Traditional
Cherokee Artisans Resources p
rogram (RTCAR), which is funded by the Cherokee Preservation
Foundation.
During the seminar, he talked about our

outreach effort in respect to butternut
activities

at the Ravensford School, ate lunch with the

Ravensford High School

forestry class
students,

and

discuss
ed

the forthcoming outreach effort.


The PI’s will continue discussions and planning for the outreach effort over the next quarter b
y
traveling to Cherokee (SS) to
me
et with Dr. Monteith, the Ravensford School’s forestry
instructor, and
repr
esentatives from the
USDI
Bureau of Indian Affairs

forestry and
Eastern
Band of Cherokee Indi
ans Natural Resources office. The purpose of the visit will be to develop
a draft of age
-
appropriate classroom exercises, inventory available equipment, and stren
gthen
external support.
The outreach effort will attempt to engage the BIA and Tribe foresters in
certain field activities. The RTCAR program will be approached to fund any
minor
equipment
needed by the Ravensford School in conjunction with this

outreach

effort.
PI Romero
-
Severson
has

spoken to two

Notre Dame teaching faculty (Michelle Whaley and Kristen Lewis) who do
science lab outreach for middle and high school students in underserved schools in South Bend.
They have agreed
to
serve as advisors to u
s if needed as we develop labs and outdoor activities.


PSU / UWA: Summer Internship for Students at PSU

PSU:

Planning was completed for the summer research visit by
Dr. Ketia Shumaker and two
undergraduate
students from the University of West Alabama
. They will conduct research on the
response of Northern red oak to ozone stress, under the supervision of the PI and his post
-
doctoral fellow Theodora Best.


UWA:

As part of the comparative hardwood genomics project’s outreach and education
component,
The University of West Alabama’s (UWA) Associate Professor, Dr. Ketia
Shumaker, is serving as coordinator, researcher, and student mentor for the summer research
internship program at Pennsylvania State University (PSU). In the fall of 2010
,

Shumaker
deve
loped an internship application (refer to the last page of this report) and coordinated a
faculty review committee composed of UWA faculty members from the biology and chemistry
departments. Starting in late November, emails were sent to all of our scienc
e majoring students
about the summer internship at PSU. Verbal announcements were also made in lecture classes
and biology club meetings. African American students were especially targeted in these
announcements. The review committee met to discuss the a
pplicants and during the first week
of March students were contacted of their acceptance status. Selected students had two days to
acceptance the offer and sign a commitment contract.
In April, Shumaker had an information dinner
meeting with the students’

parents on UWA’s
campus. Shumaker will travel with undergraduate
students Dantria Grace and Christen Nelms on June
1
st

to start their 10
-
week summer research experience
at PSU.


Photo Key : The University of West Alabama faculty
Dr. Ketia Shumaker (ce
nter) and undergraduate
students Dantria Grace (left) and Christen
Nelms
(right)
.
Grace is
a junior majoring in biology and
Nelms is a first semester senior majoring in chemistry.



Newsletter

The project manager and PI’s developed and distributed the fi
rst project newsletter describing
the project goals and personnel within a month of project initiation. It was distributed to over
200 recipients by email, and will be permanently hosted on the public website.


Presentations/Posters/Publications related

to project activities


Schlarbaum, S. E. 2011. Treats from Exotic Pests to Appalachian Forests. Gathering Places
Seminar Series, Revitalization of Traditional Cherokee Artisan Resources program, Cherokee
Preservation Foundation.

1 April 2011. (approximately 80 attendees representing the Eastern
Band of Cherokee Indians, USDI Bureau of Indian Affairs, North Carolina State Extension
Service, Ravensford School, and private individuals).


Coggeshall, M.V. 2011. TCD screening strategi
es: The search for resistance in black walnut.
Thousand Cankers Disease Workshop at Purdue University. 31 March 2011. Sponsored by
USDA Forest Service, Northern Research Station, Hardwood Tree Improvement and
Regeneration Center and Walnut Council. (80 att
endees representing 18 states).


Coggeshall, M.V. 2011. The black walnut breeding program at the University of Missouri Center
for Agroforestry. 9 April 2011. Michigan Nut Growers Association Spring Meeting in East
Lansing, MI. (60 attendees).


Gailing, O
.

2011. Development of genomic resources in oaks to study local adaptation to
drought. (8th Annual Cottonwood Symposium, February 23
-
25. Flagstaff. USA. Attendance: ~
50 scientist
s

including graduate students from the US and Canada.


(In Press)
H. Liang
, S. Ayyampalayam, N. Wickett, A. Barakat, Y. Xu*, L Landherr, P. Ralph,
T. Xu*, S.E. Schlarbaum, J. H. Leebens
-
Mack, C.W. dePamphilis. Generation of a large
-
scale
genomic resource for functional and comparative genomics in
Liriodendron
.
Tree Genetics and
Genome
. DOI: 10.1007/s11295
-
011
-
0386
-
2


(In Press) Y. Jiao, N. Wickett, S. Ayyampalayam, A. Chanderbali, L. Landherr, P.E. Ralph, L.P.
Tomsho,
H. Liang
, P.S. Soltis, D.E. Soltis, S.E. Clifton, S.E. Schlarblum, S.C. Shuster, H. Ma,
J. Leebens
-
Mack, C.W. de
Pamphilis. Phylogenomic detection of ancient polyploidy in seed
plants and angiosperms.
Nature
.
(http://www.nature.com/nature/journal/vaop/ncurrent/pdf/nature09916.pdf)


PI Carlson
and co
-
PI Jeanne Romero
-
Severson presented the project and discussed intern
ational

collaborations at the
FoResTTraC Workshop on Genomics of Forest and Ecosystem Health in
the Fagaceae held
February 23
-
25, 2011

at

INRA Headquarters

in Paris, France.




Project Management


PI Carlson (PSU)

PI Carlson’s activities in Quarter 1 fo
cused on working with Sponsored Programs at Penn State
to secure transfer of the funding for year one and setting up the main research account, the sub
-
awards to the 6 partner institutions, and the contract to support the project manager, Dr. Nicholas
Whee
ler.

A one day meeting of the project parti
cipants
was convened on Jan

15, 2010, prior to the
Plant
and Animal Genome Conference

XIX
. At the organizational meeting
revised project objectives,
respo
nsibilities, budgets, and time frames as accepted by NSF were reviewed, along with
pre
-
award research
results by the project participants. The team set p
riorities and milestones for year
one
of the project. We s
tart
ed

planning
our
outreach and education a
ctivities

and covered
publication

and data release policies
. Finally plans were laid for
the project
’s

web site
content.
Subsequent to the organizational meeting in January, a steady stream of emails and calls have
ensued among project members to discuss
questions and opportunities arising at this early stage
in the project.

Project Manager


(Wheeler, PSU)

A project management website (Basecamp) was established within weeks of the project
obtaining approved funding. This site has been used extensively

by project personnel to post and
review documents, conduct and archive discussions about
on
-
going activities, and communicate
milestones and to
-
do lists.


The projects first Newsletter was drafted and released. These will follow on an every other
quarte
r basis.

Planning for the first annual project meeting was also conducted during this quarter
. The
meeting will be held
July 10, 2011,
at the Mont Alto campus of Penn State University, in
conjunction with the Schatz Genetic Colloquium that will follow.


This first meeting is being
held at the mid
-
point of year one so that we can benefit from feedback by the SAB on our
research plans and milestones early enough for modifications to be made as needed.

P
roject progress is being maintained on a quarterly basis to insure all project personnel are aware
of activities across the group, and so that we can respond in a timely manner to potential issues
or pitfalls. Reports will be archived on our Basecamp site

and executive summaries made
available to NSF personnel.

The project manager will work with PI Romero
-
Severson to set up and conduct frequent
conference calls among all PIs working on genetic/QTL mapping projects. Project wide
conference calls have and
will continue to be called as needed.




Project Personnel


Students, Post
-
Doctoral Fellows, Staff


Clemson

Lanae Neild

is the new systems administrator at Clemson University Genomics Institute. She
earned her MS degree in Computer Science at Clemson University in 2004. She is responsible
for maintaining the web server and other computational equipment. Her expertise in

Drupal
website development will be instrumental in building the project website and expanding the
Tripal software package.


A Ph.D.
student
was recruited for the fall of 2011

to work with Dr. Liang
.


Michigan Technological University

The following student
s are working directly on the project or related projects at MTU.


o

Jennifer Lind (PhD student, funded by MTU): Local genetic adaptation in Quercus
rubra (anticipated date of graduation: fall 2013)


o

Alexis Sullivan (Master student, funded by the
Atlantis

program, Forest service,
Hanes Fund), Hybridization and local adaptation in Quercus rubra and Q.
ellipsoidalis (anticipated date of graduation: spring 2013)


o

Jessica Goodin (Master student) Adaptation of Ceratonia silqua EST
-
SSRs for
Gleditsia triacanthos
(anticipated date of graduation: spring 2012)


o

Erin Hickey (undergraduate), Adaptation of Querus robur EST
-
SSRs for Quercus
rubra







Table 1.
Time table for project activities
:
(values in boxes
are
% work completed
;

,
finishing point
s
)

RESEARCH
ACTIVITIES

-
1

Year 1

Year 2

Year 3

Year 4

Q4

Q1

Q2

Q3

Q4

Q1

Q2

Q3

Q4

Q1

Q2

Q3

Q4

Q1

Q2

Q3

Q4

Northern red oak


















Treatments; RNA isol’n


50
















EST
sequencing




















High Density Map
ping



















BAC library

construct



















Black walnut


















Treatments; RNA isol’n


100
















EST
sequencing




















High Density Map
ping



















BAC library

construct



















Sweetgum


















Treatments; RNA isol’n


















EST
sequencing




















Framework
genetic m
ap



















BAC library

construct



















Honey Locust


















Treatments; RNA isol’n


















EST
sequencing




















Framework genetic m
ap



















BAC library

construct



















Sugar maple


















Treatments; RNA isol’n


















EST
sequencing




















BAC library

construct



















Green Ash


















Treatments; RNA isol’n


















EST
sequencing




















BAC library

construct



















Tulip poplar


















Framework Map




















OUTREACH PROJECTS

Year 1

Year 2

Year 3

Year 4

Q1

Q2

Q3

Q4

Q1

Q2

Q3

Q4

Q1

Q2

Q3

Q4

Q1

Q2

Q3

Q4

Cherokee Central Schools

















Planning with Monteith

















Preparation of materials

















Summer project with students

















Evaluation and redesign

















Integration into curriculum

















Summer project with students

















Evaluation, integration, redesign

















Integrated projects with students

















Evaluation, long term planning

















University of West Alabama

















Training
workshop at PSU

















Summer research at PSU

















Attend ASPB Conference



















Table 2.
Yearly goals with participant roles

(blackened boxes)

Participants:

JEC

SES

JRS

MVC

OG

KLS

HL

MS

Goals:

Year 1









Oak and walnut seedling treatments and
RNA isolations









Finish Oak
EST sequencing









Start oak and walnut genetic
maps









Start oak and walnut
BAC libraries









Website development









Reference population development









Cherokee Central Schools outreach









Student summer research at PSU









Year 2









Sweetgum and honeylocust

seedling
treatments and RNA isolations









Finish walnut, sweetgum, and honeylocust
EST sequencing









Finish oak, walnut
BAC libraries









Continue oak, walnut genetic
maps









Start yellow
-
poplar genetic
map









Start sweetgum, honeylocust

BACs









Start maple and green ash
seedling treatments
and RNA isolations









Reference population development









Website development; EST analysis









Cherokee Central Schools outreach









Student summer research at PSU









Year 3









Finish maple and green ash
seedling
treatments and RNA isolations









Finish maple EST sequencing









Finish oak, walnut genetic
maps









Finish yellow
-
poplar genetic
map









Finish sweetgum, honeylocust

BAC libraries









Start maple and green ash ESTs









Start maple, green ash BAC libraries









Start sweetgum, honeylocust
maps









Website development; EST analysis









Cherokee Central Schools outreach









Student summer research at PSU









Year 4









Finish green ash EST sequencing









Finish sweetgum, honeylocust genetic maps









Finish
maple, green ash BAC libraries









Website development; EST analysis









Cherokee Central Schools outreach









Student summer research at PSU









Abbreviations
: JEC,
John E. Carlson
; SES,
Scott E. Schlarbaum
; JRS,
Jeanne
Romero
-
Severson
; MVC,
Mark
V

Coggeshall
; HL,
Haiying Liang
; OG,
Oliver

Gailing; KLS,
Ketia L. Shumaker; MS
,
Meg Staton;

UWA,
University West Alabama; PSU, Penn State University